Evidence map›Paper›PMID 29618770›Full record

ArticleThe Journal of antibiotics2018

Reclassification of Nocardia species based on whole genome sequence and associated phenotypic data.

Tomohiko Tamura, Shoko Ohji, Natsuko Ichikawa, Akira Hosoyama, Atsushi Yamazoe, Moriyuki Hamada, Hisayuki Komaki, Chiyo Shibata, Tetsuhiro Matsuzawa, Tohru Gonoi and 2 more

Abstract read
PubMed Publisher
In one paragraph

Article in The Journal of antibiotics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
9citing papers in PubMed, 1 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

9 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
  2. Article
  3. Review
  4. Article
  5. International journal of systematic and evolutionary microbiology · 2020
    Article
  6. Assessment of VITEK® MS IVD database V3.0 for identification of Nocardia spp. using two culture media and comparing direct smear and protein extraction procedures.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2020
    Article
  7. Review
  8. Bioactive molecules from Nocardia: diversity, bioactivities and biosynthesis.Journal of industrial microbiology & biotechnology · 2019
    Review
  9. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors.

Tomohiko TamuraBiological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan. tamura-tomohiko@nite.go.jp.ORCID http://orcid.org/0000-0003-2755-3273
Shoko OhjiBiological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-49-10 Nishihara, Shibuya-ku, Tokyo, 151-0066, Japan.
Natsuko IchikawaBiological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-49-10 Nishihara, Shibuya-ku, Tokyo, 151-0066, Japan.
Akira HosoyamaBiological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-49-10 Nishihara, Shibuya-ku, Tokyo, 151-0066, Japan.
Atsushi YamazoeBiological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan.
Moriyuki HamadaBiological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan.ORCID http://orcid.org/0000-0001-8239-6296
Hisayuki KomakiBiological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan.
Chiyo ShibataBiological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan.
Tetsuhiro MatsuzawaMedical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Chiba, 260-8673, Japan.
Tohru GonoiMedical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Chiba, 260-8673, Japan.
Ken-Ichiro SuzukiBiological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan.
Nobuyuki FujitaBiological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-49-10 Nishihara, Shibuya-ku, Tokyo, 151-0066, Japan.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Type strains of 72 validated Nocardia species were phylogenetically analyzed based on the multilocus sequence analysis (MLSA) concatenated atpD-groL1-groL2-recA-rpoA-secY-sodA-ychF. Furthermore, their similarity based on digital DNA-DNA hybridization (dDDH) was calculated. Nocardia soli, Nocardia cummidelens and Nocardia salmonicida, Nocardia nova and Nocardia elegans, Nocardia exalbida and Nocardia gamkensis, and Nocardia coubleae and Nocardia ignorata formed coherent clades, respectively. Moreover, each set showed over 70% relatedness by dDDH and shared common phenotypic characteristics. Therefore, we propose a reclassification of Nocardia soli and Nocardia cummidelens as a later heterotypic synonym of Nocardia salmonicida, Nocardia elegans as a later heterotypic synonym of Nocardia nova, Nocardia gamkensis as a later heterotypic synonym of Nocardia exalbida, and Nocardia coubleae as a later heterotypic synonym of Nocardia ignorata.

Indexed as

Bacterial Typing TechniquesDNA, BacterialGenome, BacterialGenotypeMultilocus Sequence TypingNocardiaPhenotypePhylogenyWhole Genome SequencingDNA, Bacterial

Identifiers

PMID29618770

What OpenQuestion holds

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Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.